Judging by your 2nd pic that side of the tank wasn't damaged? Saying that because of the "ninja" sticker on that side versus the other side without one. If that's so then yes that side will look close because there was no color(base) sprayed on it. Only clear.
Clearing your fairings is not going to change anything color wise. The fact they said that to you is a red flag to me like I said in my above post.
I have a lot of experience matching/bending over the years and I have never seen clear change any color to any significant degree. I have heard some of the Shop Mangers I've worked for over the years say that to Customers though.
So it's back to color match. If I was doing the job for you, I would have only a couple of options to get a color close enough to blend. First would be to try and find the factory paint code for that bike. Call the dealer first, and see if they have it using the VIN of your bike. Then see if the paint manufacturer I use has a formula for that code. If they do then chances are that will be what we call a "blendable match" as there is not as much color variation (different shades of a single color aka variances) in bike colors as there are in Cars. Plus you have the frame rail as a break so if you can get a close enough match it will work.
If I couldn't get the factory code or there was no formula for it, you are left with using the camera (spectraphotometer) or matching the color via sample chips.
The current generation of cameras work very well. We got a new one (Axalta) at the last collision shop I was at, when we switched lines from PPG to Axalta, and it was light years better than the PPG Prophet that I had earlier experience with. So that would be my choice and chances are the current generation of cameras would give a blendable match. I take multiple shots with the tool over several areas. Then mix and spray out (on a card) the color options it gives me. Compare it to the bike and go from there.
Like I said above find a good quality collision shop. They will have the most experience matching and blending color.